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It depends on what do you mean.
There's a tool called transset-df which is capable of setting the transparency level of a given window, provided that you know the window id. There's a number of ways to get that programatically, this is something that some people have done in the past in fvwm just to give you an example.
Whether that will have an impact on the window itself depends on whether your environment supports compositing. To put it plainly, it will only work if your video driver and your X server support it and are configured to enable the functionality, and provided as well that you have a compositing manager like xcompmgr or a capable window manager running like compiz, metacity or kwin.
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